Re: [ccp4bb] Space group R32 and H32
7;building' > >> and that is also its standard symbol. It describes the object without > >> reference to its orientation or position and so is not relevant to the > >> practical problem of defining the view of the building: for that you > >> need extra symbols. For example you might need to specify one of the > >> setting symbols 'building (front elevation)', 'building (side > >> elevation)' or 'building (plan)'. > >> > >> So R32 is a H-M standard symbol which corresponds to the 2 alternate > >> setting symbols R32:r and R32:h as described in the article. Plainly > >> you can't use the H-M symbol R32 to uniquely specify the setting since > >> it is the standard symbol for both the R32:r and R32:h settings. The > >> latter are _not_ H-M symbols: they are ITC extensions of the H-M > >> symbol. > >> > >> For other space groups further confusion has arisen because ITC often > >> uses the exact same character string for both the standard symbol and > >> one of the corresponding alternate setting symbols. An obvious > >> example is P21212: this is the H-M standard symbol for SG #18 but is > >> also one of the 3 ITC setting symbols for P21212, the other two being > >> P22121 and P21221. Perhaps the intention would have been clearer if > >> the ITC setting symbols had all been made different from the standard > >> symbol, as they are in the R32 case. For example P21212a, P21212b and > >> P21212c would have been equally valid choices for the ITC setting > >> symbols but do not express a 'preferred' setting (since there isn't > >> one). Similarly the standard symbol for SG #5 (unique axis b) is C2, > >> and the alternate setting symbols are A2, C2 and I2, but they could > >> equally well have been (for example) C2a, C2c and C2i, which doesn't > >> express a preference for any one of the alternate settings. > >> > >> Either way, according to the ITC rules, the choice of 'conventional' > >> setting for a space group (i.e. the recommended default choice when > >> there are no other grounds such as isomorphism with a previously > >> determined structure) is made by reference to the unit cell. For R32 > >> the conventional cell happens to be the hexagonal one (a = b != c, > >> alpha = beta = 90, gamma = 120) with symbol R32:h; for all > >> orthorhombic SGs the convention is a < b < c and the setting symbol > >> derives from that. > >> > >> Cheers > >> > >> -- Ian > >> > >> On 28 July 2012 22:22, Edward A. Berry wrote: > >> > Are all the software packages consistent in their (mis)use of these > >> > symbols? Recently I scaled data (scalepack) as R3, imported to ccp4 as > >> > H3, > >> > and had to make a link in $ODAT/symm from R32 to H32 (which it turned > >> > out to > >> > be). > >> > > >> > > >> > > >> > Ian Tickle wrote: > >> >> > >> >> If we're all agreed that ITC(A) is taken as the authority on all > >> >> matters of space group symbology (and I for one certainly agree that > >> >> it should be), then SG symbol H32 (SG #145: > >> >> http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do > >> >> with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)! > >> >> According to the Hermann-Mauguin system of nomenclature H32 (more > >> >> correctly written as H3_2 where the '_' indicates a subscripted screw > >> >> axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2 > >> >> in H-M). H32 as an alternate setting symbol for R32 is a very recent > >> >> PDB invention which conflicts with the well-established H-M convention > >> >> used throughout ITC. The ITC symbols for the rhombohedral& hexagonal > >> >> > >> >> axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious > >> >> extensions of the H-M symbols without introducing any conflict with > >> >> the existing convention, as the PDB symbol does. The confusion has > >> >> arisen from the failure to distinguish the lattice type (the first > >> >> letter of the symbol) from the symbol for the basis system of the > >> >> setting (the final letter after the ':'). > >> >> > >> >> See http://cci.lbl.g
Re: [ccp4bb] Space group R32 and H32
gt; > >> > >> > >> > Ian Tickle wrote: >> >> >> >> If we're all agreed that ITC(A) is taken as the authority on all >> >> matters of space group symbology (and I for one certainly agree that >> >> it should be), then SG symbol H32 (SG #145: >> >> http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do >> >> with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)! >> >> According to the Hermann-Mauguin system of nomenclature H32 (more >> >> correctly written as H3_2 where the '_' indicates a subscripted screw >> >> axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2 >> >> in H-M). H32 as an alternate setting symbol for R32 is a very recent >> >> PDB invention which conflicts with the well-established H-M convention >> >> used throughout ITC. The ITC symbols for the rhombohedral& hexagonal >> >> >> >> axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious >> >> extensions of the H-M symbols without introducing any conflict with >> >> the existing convention, as the PDB symbol does. The confusion has >> >> arisen from the failure to distinguish the lattice type (the first >> >> letter of the symbol) from the symbol for the basis system of the >> >> setting (the final letter after the ':'). >> >> >> >> See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an >> >> excellent explanation of all this and of the confusion that arises >> >> when programmers ignore established conventions and 're-invent the >> >> wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols >> >> R32& H32 and uses R32 for PDB H32 and vice-versa!). >> >> >> >> >> >> Cheers >> >> >> >> -- Ian >> >> >> >> On 27 July 2012 21:09, Bernhard Rupp wrote: >> >>> >> >>> H32 indicates the hexagonal obverse setting (as you list) for a R >> >>> centered trigonal cell, which is 3x larger than the primitive R32 cell >> >>> indexed a=b=c, al=be=ga<> 90. Standard imho is the H32 setting, for >> >>> which I >> >>> will probably get flamed. >> >>> The relation between H and R cells is depicted here: >> >>> >> >>> http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm >> >>> >> >>> This has been discussed and is explained in the ccp4 tutorials and doc >> >>> afaik, where you can find more detailed info. >> >>> >> >>> For proper format in a journal, I would suggest to adhere to the format >> >>> given in the ITC (International tables for Crystallography), I.e. Bravais >> >>> Italic, subscripted screw symbols. Note that this is not the format you >> >>> put >> >>> it into most programs - their docs help. >> >>> >> >>> You can also try my old space croup decoding program to see general >> >>> positions, operators, matrices and other useful stuff. >> >>> >> >>> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm >> >>> >> >>> HTH, BR >> >>> >> >>> -Original Message- >> >>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> >>> Theresa Hsu >> >>> Sent: Friday, July 27, 2012 12:54 PM >> >>> To: CCP4BB@JISCMAIL.AC.UK >> >>> Subject: [ccp4bb] Space group R32 and H32 >> >>> >> >>> Dear all >> >>> >> >>> I have a confusion on the space group R32 and H32. For a cell parameter >> >>> of a = b not equal to c, alpha=beta, not equal to gamma, is it >> >>> considered as >> >>> R32 or H32? >> >>> >> >>> I tried searching the mail list archives but it does not help a beginner >> >>> crystallographer like me. >> >>> >> >>> I also have another basic question. What is the correct way for writing >> >>> space groups? Is the Bravais lattice in italic and is there space after >> >>> that? Or it does not matter because both are used in literature? >> >>> >> >>> Thank you. >> >> >> >> >> > > > -- > > === > * * > * Gerard Bricogne g...@globalphasing.com * > * * > * Global Phasing Ltd. * > * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * > * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * > * * > ===
Re: [ccp4bb] Space group R32 and H32
e > setting symbols R32:r and R32:h as described in the article. Plainly > you can't use the H-M symbol R32 to uniquely specify the setting since > it is the standard symbol for both the R32:r and R32:h settings. The > latter are _not_ H-M symbols: they are ITC extensions of the H-M > symbol. > > For other space groups further confusion has arisen because ITC often > uses the exact same character string for both the standard symbol and > one of the corresponding alternate setting symbols. An obvious > example is P21212: this is the H-M standard symbol for SG #18 but is > also one of the 3 ITC setting symbols for P21212, the other two being > P22121 and P21221. Perhaps the intention would have been clearer if > the ITC setting symbols had all been made different from the standard > symbol, as they are in the R32 case. For example P21212a, P21212b and > P21212c would have been equally valid choices for the ITC setting > symbols but do not express a 'preferred' setting (since there isn't > one). Similarly the standard symbol for SG #5 (unique axis b) is C2, > and the alternate setting symbols are A2, C2 and I2, but they could > equally well have been (for example) C2a, C2c and C2i, which doesn't > express a preference for any one of the alternate settings. > > Either way, according to the ITC rules, the choice of 'conventional' > setting for a space group (i.e. the recommended default choice when > there are no other grounds such as isomorphism with a previously > determined structure) is made by reference to the unit cell. For R32 > the conventional cell happens to be the hexagonal one (a = b != c, > alpha = beta = 90, gamma = 120) with symbol R32:h; for all > orthorhombic SGs the convention is a < b < c and the setting symbol > derives from that. > > Cheers > > -- Ian > > On 28 July 2012 22:22, Edward A. Berry wrote: > > Are all the software packages consistent in their (mis)use of these > > symbols? Recently I scaled data (scalepack) as R3, imported to ccp4 as H3, > > and had to make a link in $ODAT/symm from R32 to H32 (which it turned out to > > be). > > > > > > > > Ian Tickle wrote: > >> > >> If we're all agreed that ITC(A) is taken as the authority on all > >> matters of space group symbology (and I for one certainly agree that > >> it should be), then SG symbol H32 (SG #145: > >> http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do > >> with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)! > >> According to the Hermann-Mauguin system of nomenclature H32 (more > >> correctly written as H3_2 where the '_' indicates a subscripted screw > >> axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2 > >> in H-M). H32 as an alternate setting symbol for R32 is a very recent > >> PDB invention which conflicts with the well-established H-M convention > >> used throughout ITC. The ITC symbols for the rhombohedral& hexagonal > >> > >> axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious > >> extensions of the H-M symbols without introducing any conflict with > >> the existing convention, as the PDB symbol does. The confusion has > >> arisen from the failure to distinguish the lattice type (the first > >> letter of the symbol) from the symbol for the basis system of the > >> setting (the final letter after the ':'). > >> > >> See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an > >> excellent explanation of all this and of the confusion that arises > >> when programmers ignore established conventions and 're-invent the > >> wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols > >> R32& H32 and uses R32 for PDB H32 and vice-versa!). > >> > >> > >> Cheers > >> > >> -- Ian > >> > >> On 27 July 2012 21:09, Bernhard Rupp wrote: > >>> > >>> H32 indicates the hexagonal obverse setting (as you list) for a R > >>> centered trigonal cell, which is 3x larger than the primitive R32 cell > >>> indexed a=b=c, al=be=ga<> 90. Standard imho is the H32 setting, for > >>> which I > >>> will probably get flamed. > >>> The relation between H and R cells is depicted here: > >>> > >>> http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm > >>> > >>> This has been discussed and is explained in the ccp4 tutorials and doc > >>> afaik, wher
Re: [ccp4bb] Space group R32 and H32
he ITC setting >> symbols but do not express a 'preferred' setting (since there isn't >> one). Similarly the standard symbol for SG #5 (unique axis b) is C2, >> and the alternate setting symbols are A2, C2 and I2, but they could >> equally well have been (for example) C2a, C2c and C2i, which doesn't >> express a preference for any one of the alternate settings. >> >> Either way, according to the ITC rules, the choice of 'conventional' >> setting for a space group (i.e. the recommended default choice when >> there are no other grounds such as isomorphism with a previously >> determined structure) is made by reference to the unit cell. For R32 >> the conventional cell happens to be the hexagonal one (a = b != c, >> alpha = beta = 90, gamma = 120) with symbol R32:h; for all >> orthorhombic SGs the convention is a < b < c and the setting symbol >> derives from that. >> >> Cheers >> >> -- Ian >> >> On 28 July 2012 22:22, Edward A. Berry wrote: >> >> Are all the software packages consistent in their (mis)use of these >> >> symbols? Recently I scaled data (scalepack) as R3, imported to ccp4 as H3, >> >> and had to make a link in $ODAT/symm from R32 to H32 (which it turned out to >> >> be). >> >> >> >> >> Ian Tickle wrote: >> >> >> If we're all agreed that ITC(A) is taken as the authority on all >> >> matters of space group symbology (and I for one certainly agree that >> >> it should be), then SG symbol H32 (SG #145: >> >> http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do >> >> with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)! >> >> According to the Hermann-Mauguin system of nomenclature H32 (more >> >> correctly written as H3_2 where the '_' indicates a subscripted screw >> >> axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2 >> >> in H-M). H32 as an alternate setting symbol for R32 is a very recent >> >> PDB invention which conflicts with the well-established H-M convention >> >> used throughout ITC. The ITC symbols for the rhombohedral& hexagonal >> >> >> axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious >> >> extensions of the H-M symbols without introducing any conflict with >> >> the existing convention, as the PDB symbol does. The confusion has >> >> arisen from the failure to distinguish the lattice type (the first >> >> letter of the symbol) from the symbol for the basis system of the >> >> setting (the final letter after the ':'). >> >> >> See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an >> >> excellent explanation of all this and of the confusion that arises >> >> when programmers ignore established conventions and 're-invent the >> >> wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols >> >> R32& H32 and uses R32 for PDB H32 and vice-versa!). >> >> >> >> Cheers >> >> >> -- Ian >> >> >> On 27 July 2012 21:09, Bernhard Rupp wrote: >> >> >> H32 indicates the hexagonal obverse setting (as you list) for a R >> >> centered trigonal cell, which is 3x larger than the primitive R32 cell >> >> indexed a=b=c, al=be=ga<> 90. Standard imho is the H32 setting, for which I >> >> will probably get flamed. >> >> The relation between H and R cells is depicted here: >> >> >> http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm >> >> >> This has been discussed and is explained in the ccp4 tutorials and doc >> >> afaik, where you can find more detailed info. >> >> >> For proper format in a journal, I would suggest to adhere to the format >> >> given in the ITC (International tables for Crystallography), I.e. Bravais >> >> Italic, subscripted screw symbols. Note that this is not the format you put >> >> it into most programs - their docs help. >> >> >> You can also try my old space croup decoding program to see general >> >> positions, operators, matrices and other useful stuff. >> >> >> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm >> >> >> HTH, BR >> >> >> -Original Message- >> >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> >> Theresa Hsu >> >> Sent: Friday, July 27, 2012 12:54 PM >> >> To: CCP4BB@JISCMAIL.AC.UK >> >> Subject: [ccp4bb] Space group R32 and H32 >> >> >> Dear all >> >> >> I have a confusion on the space group R32 and H32. For a cell parameter >> >> of a = b not equal to c, alpha=beta, not equal to gamma, is it considered as >> >> R32 or H32? >> >> >> I tried searching the mail list archives but it does not help a beginner >> >> crystallographer like me. >> >> >> I also have another basic question. What is the correct way for writing >> >> space groups? Is the Bravais lattice in italic and is there space after >> >> that? Or it does not matter because both are used in literature? >> >> >> Thank you. >> >> >> >> >> >> -- >> Sebastiano Pasqualato, PhD >> Crystallography Unit >> Department of Experimental Oncology >> European Institute of Oncology >> IFOM-IEO Campus >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5167 >> fax +39 02 9437 5990 >> >> please note the change in email address! >> sebastiano.pasqual...@ieo.eu >> >> >> >> >> >> >> -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
Re: [ccp4bb] Space group R32 and H32
oice when > there are no other grounds such as isomorphism with a previously > determined structure) is made by reference to the unit cell. For R32 > the conventional cell happens to be the hexagonal one (a = b != c, > alpha = beta = 90, gamma = 120) with symbol R32:h; for all > orthorhombic SGs the convention is a < b < c and the setting symbol > derives from that. > > Cheers > > -- Ian > > On 28 July 2012 22:22, Edward A. Berry wrote: > > Are all the software packages consistent in their (mis)use of these > > symbols? Recently I scaled data (scalepack) as R3, imported to ccp4 as H3, > > and had to make a link in $ODAT/symm from R32 to H32 (which it turned out to > > be). > > > > > Ian Tickle wrote: > > > If we're all agreed that ITC(A) is taken as the authority on all > > matters of space group symbology (and I for one certainly agree that > > it should be), then SG symbol H32 (SG #145: > > http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do > > with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)! > > According to the Hermann-Mauguin system of nomenclature H32 (more > > correctly written as H3_2 where the '_' indicates a subscripted screw > > axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2 > > in H-M). H32 as an alternate setting symbol for R32 is a very recent > > PDB invention which conflicts with the well-established H-M convention > > used throughout ITC. The ITC symbols for the rhombohedral& hexagonal > > > axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious > > extensions of the H-M symbols without introducing any conflict with > > the existing convention, as the PDB symbol does. The confusion has > > arisen from the failure to distinguish the lattice type (the first > > letter of the symbol) from the symbol for the basis system of the > > setting (the final letter after the ':'). > > > See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an > > excellent explanation of all this and of the confusion that arises > > when programmers ignore established conventions and 're-invent the > > wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols > > R32& H32 and uses R32 for PDB H32 and vice-versa!). > > > > Cheers > > > -- Ian > > > On 27 July 2012 21:09, Bernhard Rupp wrote: > > > H32 indicates the hexagonal obverse setting (as you list) for a R > > centered trigonal cell, which is 3x larger than the primitive R32 cell > > indexed a=b=c, al=be=ga<> 90. Standard imho is the H32 setting, for which I > > will probably get flamed. > > The relation between H and R cells is depicted here: > > > http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm > > > This has been discussed and is explained in the ccp4 tutorials and doc > > afaik, where you can find more detailed info. > > > For proper format in a journal, I would suggest to adhere to the format > > given in the ITC (International tables for Crystallography), I.e. Bravais > > Italic, subscripted screw symbols. Note that this is not the format you put > > it into most programs - their docs help. > > > You can also try my old space croup decoding program to see general > > positions, operators, matrices and other useful stuff. > > > http://www.ruppweb.org/new_comp/spacegroup_decoder.htm > > > HTH, BR > > > -Original Message- > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > > Theresa Hsu > > Sent: Friday, July 27, 2012 12:54 PM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: [ccp4bb] Space group R32 and H32 > > > Dear all > > > I have a confusion on the space group R32 and H32. For a cell parameter > > of a = b not equal to c, alpha=beta, not equal to gamma, is it considered as > > R32 or H32? > > > I tried searching the mail list archives but it does not help a beginner > > crystallographer like me. > > > I also have another basic question. What is the correct way for writing > > space groups? Is the Bravais lattice in italic and is there space after > > that? Or it does not matter because both are used in literature? > > > Thank you. > > > > > > -- > Sebastiano Pasqualato, PhD > Crystallography Unit > Department of Experimental Oncology > European Institute of Oncology > IFOM-IEO Campus > via Adamello, 16 > 20139 - Milano > Italy > > tel +39 02 9437 5167 > fax +39 02 9437 5990 > > please note the change in email address! > sebastiano.pasqual...@ieo.eu > > > > > > >
Re: [ccp4bb] Space group R32 and H32
> >> >> Ian Tickle wrote: >>> >>> If we're all agreed that ITC(A) is taken as the authority on all >>> matters of space group symbology (and I for one certainly agree that >>> it should be), then SG symbol H32 (SG #145: >>> http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do >>> with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)! >>> According to the Hermann-Mauguin system of nomenclature H32 (more >>> correctly written as H3_2 where the '_' indicates a subscripted screw >>> axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2 >>> in H-M). H32 as an alternate setting symbol for R32 is a very recent >>> PDB invention which conflicts with the well-established H-M convention >>> used throughout ITC. The ITC symbols for the rhombohedral& hexagonal >>> >>> axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious >>> extensions of the H-M symbols without introducing any conflict with >>> the existing convention, as the PDB symbol does. The confusion has >>> arisen from the failure to distinguish the lattice type (the first >>> letter of the symbol) from the symbol for the basis system of the >>> setting (the final letter after the ':'). >>> >>> See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an >>> excellent explanation of all this and of the confusion that arises >>> when programmers ignore established conventions and 're-invent the >>> wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols >>> R32& H32 and uses R32 for PDB H32 and vice-versa!). >>> >>> >>> Cheers >>> >>> -- Ian >>> >>> On 27 July 2012 21:09, Bernhard Rupp wrote: >>>> >>>> H32 indicates the hexagonal obverse setting (as you list) for a R >>>> centered trigonal cell, which is 3x larger than the primitive R32 cell >>>> indexed a=b=c, al=be=ga<> 90. Standard imho is the H32 setting, for which >>>> I >>>> will probably get flamed. >>>> The relation between H and R cells is depicted here: >>>> >>>> http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm >>>> >>>> This has been discussed and is explained in the ccp4 tutorials and doc >>>> afaik, where you can find more detailed info. >>>> >>>> For proper format in a journal, I would suggest to adhere to the format >>>> given in the ITC (International tables for Crystallography), I.e. Bravais >>>> Italic, subscripted screw symbols. Note that this is not the format you put >>>> it into most programs - their docs help. >>>> >>>> You can also try my old space croup decoding program to see general >>>> positions, operators, matrices and other useful stuff. >>>> >>>> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm >>>> >>>> HTH, BR >>>> >>>> -Original Message- >>>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >>>> Theresa Hsu >>>> Sent: Friday, July 27, 2012 12:54 PM >>>> To: CCP4BB@JISCMAIL.AC.UK >>>> Subject: [ccp4bb] Space group R32 and H32 >>>> >>>> Dear all >>>> >>>> I have a confusion on the space group R32 and H32. For a cell parameter >>>> of a = b not equal to c, alpha=beta, not equal to gamma, is it considered >>>> as >>>> R32 or H32? >>>> >>>> I tried searching the mail list archives but it does not help a beginner >>>> crystallographer like me. >>>> >>>> I also have another basic question. What is the correct way for writing >>>> space groups? Is the Bravais lattice in italic and is there space after >>>> that? Or it does not matter because both are used in literature? >>>> >>>> Thank you. >>> >>> >> -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
Re: [ccp4bb] Space group R32 and H32
on >> used throughout ITC. The ITC symbols for the rhombohedral& hexagonal >> >> axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious >> extensions of the H-M symbols without introducing any conflict with >> the existing convention, as the PDB symbol does. The confusion has >> arisen from the failure to distinguish the lattice type (the first >> letter of the symbol) from the symbol for the basis system of the >> setting (the final letter after the ':'). >> >> See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an >> excellent explanation of all this and of the confusion that arises >> when programmers ignore established conventions and 're-invent the >> wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols >> R32& H32 and uses R32 for PDB H32 and vice-versa!). >> >> >> Cheers >> >> -- Ian >> >> On 27 July 2012 21:09, Bernhard Rupp wrote: >>> >>> H32 indicates the hexagonal obverse setting (as you list) for a R >>> centered trigonal cell, which is 3x larger than the primitive R32 cell >>> indexed a=b=c, al=be=ga<> 90. Standard imho is the H32 setting, for which I >>> will probably get flamed. >>> The relation between H and R cells is depicted here: >>> >>> http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm >>> >>> This has been discussed and is explained in the ccp4 tutorials and doc >>> afaik, where you can find more detailed info. >>> >>> For proper format in a journal, I would suggest to adhere to the format >>> given in the ITC (International tables for Crystallography), I.e. Bravais >>> Italic, subscripted screw symbols. Note that this is not the format you put >>> it into most programs - their docs help. >>> >>> You can also try my old space croup decoding program to see general >>> positions, operators, matrices and other useful stuff. >>> >>> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm >>> >>> HTH, BR >>> >>> -Original Message- >>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >>> Theresa Hsu >>> Sent: Friday, July 27, 2012 12:54 PM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: [ccp4bb] Space group R32 and H32 >>> >>> Dear all >>> >>> I have a confusion on the space group R32 and H32. For a cell parameter >>> of a = b not equal to c, alpha=beta, not equal to gamma, is it considered as >>> R32 or H32? >>> >>> I tried searching the mail list archives but it does not help a beginner >>> crystallographer like me. >>> >>> I also have another basic question. What is the correct way for writing >>> space groups? Is the Bravais lattice in italic and is there space after >>> that? Or it does not matter because both are used in literature? >>> >>> Thank you. >> >> >
Re: [ccp4bb] Space group R32 and H32
Are all the software packages consistent in their (mis)use of these symbols? Recently I scaled data (scalepack) as R3, imported to ccp4 as H3, and had to make a link in $ODAT/symm from R32 to H32 (which it turned out to be). Ian Tickle wrote: If we're all agreed that ITC(A) is taken as the authority on all matters of space group symbology (and I for one certainly agree that it should be), then SG symbol H32 (SG #145: http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)! According to the Hermann-Mauguin system of nomenclature H32 (more correctly written as H3_2 where the '_' indicates a subscripted screw axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2 in H-M). H32 as an alternate setting symbol for R32 is a very recent PDB invention which conflicts with the well-established H-M convention used throughout ITC. The ITC symbols for the rhombohedral& hexagonal axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious extensions of the H-M symbols without introducing any conflict with the existing convention, as the PDB symbol does. The confusion has arisen from the failure to distinguish the lattice type (the first letter of the symbol) from the symbol for the basis system of the setting (the final letter after the ':'). See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an excellent explanation of all this and of the confusion that arises when programmers ignore established conventions and 're-invent the wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols R32& H32 and uses R32 for PDB H32 and vice-versa!). Cheers -- Ian On 27 July 2012 21:09, Bernhard Rupp wrote: H32 indicates the hexagonal obverse setting (as you list) for a R centered trigonal cell, which is 3x larger than the primitive R32 cell indexed a=b=c, al=be=ga<> 90. Standard imho is the H32 setting, for which I will probably get flamed. The relation between H and R cells is depicted here: http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm This has been discussed and is explained in the ccp4 tutorials and doc afaik, where you can find more detailed info. For proper format in a journal, I would suggest to adhere to the format given in the ITC (International tables for Crystallography), I.e. Bravais Italic, subscripted screw symbols. Note that this is not the format you put it into most programs - their docs help. You can also try my old space croup decoding program to see general positions, operators, matrices and other useful stuff. http://www.ruppweb.org/new_comp/spacegroup_decoder.htm HTH, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa Hsu Sent: Friday, July 27, 2012 12:54 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Space group R32 and H32 Dear all I have a confusion on the space group R32 and H32. For a cell parameter of a = b not equal to c, alpha=beta, not equal to gamma, is it considered as R32 or H32? I tried searching the mail list archives but it does not help a beginner crystallographer like me. I also have another basic question. What is the correct way for writing space groups? Is the Bravais lattice in italic and is there space after that? Or it does not matter because both are used in literature? Thank you.
Re: [ccp4bb] Space group R32 and H32
If we're all agreed that ITC(A) is taken as the authority on all matters of space group symbology (and I for one certainly agree that it should be), then SG symbol H32 (SG #145: http://img.chem.ucl.ac.uk/sgp/medium/145bz1.htm) has nothing to do with R32 (SG #155: http://img.chem.ucl.ac.uk/sgp/medium/155az1.htm)! According to the Hermann-Mauguin system of nomenclature H32 (more correctly written as H3_2 where the '_' indicates a subscripted screw axis) would be the hexagonal-centred (H) lattice setting of P32 (P3_2 in H-M). H32 as an alternate setting symbol for R32 is a very recent PDB invention which conflicts with the well-established H-M convention used throughout ITC. The ITC symbols for the rhombohedral & hexagonal axis settings of SG R32 are R32:r and R32:h respectively, i.e. obvious extensions of the H-M symbols without introducing any conflict with the existing convention, as the PDB symbol does. The confusion has arisen from the failure to distinguish the lattice type (the first letter of the symbol) from the symbol for the basis system of the setting (the final letter after the ':'). See http://cci.lbl.gov/~rwgk/my_papers/CCN_2011_01_H3_H32.pdf for an excellent explanation of all this and of the confusion that arises when programmers ignore established conventions and 're-invent the wheel' (e.g. SCALEPACK apparently swaps the meaning of the PDB symbols R32 & H32 and uses R32 for PDB H32 and vice-versa!). Cheers -- Ian On 27 July 2012 21:09, Bernhard Rupp wrote: > H32 indicates the hexagonal obverse setting (as you list) for a R centered > trigonal cell, which is 3x larger than the primitive R32 cell indexed a=b=c, > al=be=ga <> 90. Standard imho is the H32 setting, for which I will probably > get flamed. > The relation between H and R cells is depicted here: > http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm > > This has been discussed and is explained in the ccp4 tutorials and doc afaik, > where you can find more detailed info. > > For proper format in a journal, I would suggest to adhere to the format given > in the ITC (International tables for Crystallography), I.e. Bravais Italic, > subscripted screw symbols. Note that this is not the format you put it into > most programs - their docs help. > > You can also try my old space croup decoding program to see general > positions, operators, matrices and other useful stuff. > > http://www.ruppweb.org/new_comp/spacegroup_decoder.htm > > HTH, BR > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa > Hsu > Sent: Friday, July 27, 2012 12:54 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Space group R32 and H32 > > Dear all > > I have a confusion on the space group R32 and H32. For a cell parameter of a > = b not equal to c, alpha=beta, not equal to gamma, is it considered as R32 > or H32? > > I tried searching the mail list archives but it does not help a beginner > crystallographer like me. > > I also have another basic question. What is the correct way for writing space > groups? Is the Bravais lattice in italic and is there space after that? Or it > does not matter because both are used in literature? > > Thank you.
Re: [ccp4bb] Space group R32 and H32
You are correct, sir. It is one lattice point for each centered face. So, for the F centered lattices which have a face centered lattice point on all faces you add 3 lattice points to the original primitive lattice point for a total of 4 lattice points. It's all in "the Tables." Cheers, Chris On 7/27/12 4:40 PM, "Bernhard Rupp" wrote: >Thanks for the translation, and a correction of the translator: > >> similar to the face or body centered lattices, which have two lattice >points per cell. > >Is this so? Ortho F and FCC have 4 Bravais vectors > >All (in full translation) in chapter 5 of BMC. > >BR > > > >
Re: [ccp4bb] Space group R32 and H32
Thanks for the translation, and a correction of the translator: > similar to the face or body centered lattices, which have two lattice points per cell. Is this so? Ortho F and FCC have 4 Bravais vectors All (in full translation) in chapter 5 of BMC. BR
Re: [ccp4bb] Space group R32 and H32
To add a little more clarity to the discussion. The hexagonal obverse setting is 3X larger because it is triply primitive. This means there are 3 lattice points per unit cell, similar to the face or body centered lattices, which have two lattice points per cell. To read BR's scripts: For the primitive Rhombohedral setting: a=b=c means a is equal to b is equal to c. al=be=ga <> 90° means alpha is equal to beta is equal to gamma, but not necessarily equal to 90°. As Harry points out, all angles can be equal to 90°, but they don't have to be. For the triply primitive Hexagonal setting: a=b, means that a is equal to b and c is unique. al=be=90°, ga=120° means that alpha and beta are equal to 90°, and gamma is 120°. Notice that the triply primitive hexagonal setting, as its name implies, has the same unit cell requirements as a hexagonal lattice. I was taught when writing the space group symbol for a manuscript the lattice type is italic, the symmetry operators are normal, and the screw axes are subscript. All are written without spaces between them. As BR points out, entry into programs is at the discretion of the program author. Of course, the International Tables has a wonderful discussion on all this and I encourage you to read it to fully understand the nomenclature. HTH, Chris On 7/27/12 3:21 PM, "Harry" wrote: >Hi > >Just to clarify - for H32, a=b<>c (though you could have a=b=c within >measurement error), alpha=beta=90º, gamma=120º. Just having alpha=beta ><> gamma is necessary but not sufficient. > >BTW, there's nothing wrong with alpha=beta=gamma=90º for the R >setting. It's just not required. > >Sorry if this isn't clear - I'm just watching a very odd Olympic >opening ceremony, and it's quite distracting! > >On 27 Jul 2012, at 21:09, Bernhard Rupp wrote: > >> H32 indicates the hexagonal obverse setting (as you list) for a R >> centered trigonal cell, which is 3x larger than the primitive R32 >> cell indexed a=b=c, al=be=ga <> 90. Standard imho is the H32 >> setting, for which I will probably get flamed. >> The relation between H and R cells is depicted here: >> >>http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallogr >>aphy_Fig_5-29.htm >> >> This has been discussed and is explained in the ccp4 tutorials and >> doc afaik, where you can find more detailed info. >> >> For proper format in a journal, I would suggest to adhere to the >> format given in the ITC (International tables for Crystallography), >> I.e. Bravais Italic, subscripted screw symbols. Note that this is >> not the format you put it into most programs - their docs help. >> >> You can also try my old space croup decoding program to see general >> positions, operators, matrices and other useful stuff. >> >> http://www.ruppweb.org/new_comp/spacegroup_decoder.htm >> >> HTH, BR >> >> -Original Message- >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf >> Of Theresa Hsu >> Sent: Friday, July 27, 2012 12:54 PM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] Space group R32 and H32 >> >> Dear all >> >> I have a confusion on the space group R32 and H32. For a cell >> parameter of a = b not equal to c, alpha=beta, not equal to gamma, >> is it considered as R32 or H32? >> >> I tried searching the mail list archives but it does not help a >> beginner crystallographer like me. >> >> I also have another basic question. What is the correct way for >> writing space groups? Is the Bravais lattice in italic and is there >> space after that? Or it does not matter because both are used in >> literature? >> >> Thank you. > >Harry >-- >Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, >Hills Road, Cambridge, CB2 0QH >
Re: [ccp4bb] Space group R32 and H32
Hi Just to clarify - for H32, a=b<>c (though you could have a=b=c within measurement error), alpha=beta=90º, gamma=120º. Just having alpha=beta <> gamma is necessary but not sufficient. BTW, there's nothing wrong with alpha=beta=gamma=90º for the R setting. It's just not required. Sorry if this isn't clear - I'm just watching a very odd Olympic opening ceremony, and it's quite distracting! On 27 Jul 2012, at 21:09, Bernhard Rupp wrote: H32 indicates the hexagonal obverse setting (as you list) for a R centered trigonal cell, which is 3x larger than the primitive R32 cell indexed a=b=c, al=be=ga <> 90. Standard imho is the H32 setting, for which I will probably get flamed. The relation between H and R cells is depicted here: http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm This has been discussed and is explained in the ccp4 tutorials and doc afaik, where you can find more detailed info. For proper format in a journal, I would suggest to adhere to the format given in the ITC (International tables for Crystallography), I.e. Bravais Italic, subscripted screw symbols. Note that this is not the format you put it into most programs - their docs help. You can also try my old space croup decoding program to see general positions, operators, matrices and other useful stuff. http://www.ruppweb.org/new_comp/spacegroup_decoder.htm HTH, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa Hsu Sent: Friday, July 27, 2012 12:54 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Space group R32 and H32 Dear all I have a confusion on the space group R32 and H32. For a cell parameter of a = b not equal to c, alpha=beta, not equal to gamma, is it considered as R32 or H32? I tried searching the mail list archives but it does not help a beginner crystallographer like me. I also have another basic question. What is the correct way for writing space groups? Is the Bravais lattice in italic and is there space after that? Or it does not matter because both are used in literature? Thank you. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Space group R32 and H32
H32 indicates the hexagonal obverse setting (as you list) for a R centered trigonal cell, which is 3x larger than the primitive R32 cell indexed a=b=c, al=be=ga <> 90. Standard imho is the H32 setting, for which I will probably get flamed. The relation between H and R cells is depicted here: http://www.ruppweb.org/Garland/gallery/Ch5/pages/Biomolecular_Crystallography_Fig_5-29.htm This has been discussed and is explained in the ccp4 tutorials and doc afaik, where you can find more detailed info. For proper format in a journal, I would suggest to adhere to the format given in the ITC (International tables for Crystallography), I.e. Bravais Italic, subscripted screw symbols. Note that this is not the format you put it into most programs - their docs help. You can also try my old space croup decoding program to see general positions, operators, matrices and other useful stuff. http://www.ruppweb.org/new_comp/spacegroup_decoder.htm HTH, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa Hsu Sent: Friday, July 27, 2012 12:54 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Space group R32 and H32 Dear all I have a confusion on the space group R32 and H32. For a cell parameter of a = b not equal to c, alpha=beta, not equal to gamma, is it considered as R32 or H32? I tried searching the mail list archives but it does not help a beginner crystallographer like me. I also have another basic question. What is the correct way for writing space groups? Is the Bravais lattice in italic and is there space after that? Or it does not matter because both are used in literature? Thank you.
[ccp4bb] Space group R32 and H32
Dear all I have a confusion on the space group R32 and H32. For a cell parameter of a = b not equal to c, alpha=beta, not equal to gamma, is it considered as R32 or H32? I tried searching the mail list archives but it does not help a beginner crystallographer like me. I also have another basic question. What is the correct way for writing space groups? Is the Bravais lattice in italic and is there space after that? Or it does not matter because both are used in literature? Thank you.
